Rediscovery of Nebela ansata (Amoebozoa: Arcellinida) in eastern North America: biogeographical implications

Aim The question whether free‐living protists are generally cosmopolitan is currently a matter of debate. In this study we investigate the geographical distribution of a distinctive testate amoeba species, Nebela ansata, and use our data to assess the potential for highly restricted distribution patterns in some protist species. Location Global. Methods We analysed (1) 3400 testate amoeba publications from North America and other continents, (2) unpublished slides of the Penard Collection of the Natural History Museum, London, UK, and (3) 104 Sphagnum samples from eastern North America. Non‐metric multidimensional scaling (NMDS) was used to visualize the similarities in testate amoeba community composition among 1012 North American samples, including two communities that contained N. ansata. Results We rediscovered N. ansata at a site in New Jersey located close to its type locality, and in Nova Scotia. We also report the existence of an apparently unpublished museum specimen originally collected from New Jersey. Our extensive literature survey confirmed the presence of this species only in the temperate part of eastern North America. The NMDS revealed that communities with N. ansata were less similar to each other than to communities from other parts of North America, suggesting that favourable habitats for N. ansata occur in other Sphagnum‐dominated peatlands, a habitat type that has been extensively sampled in North America and elsewhere. Main conclusions These data provide an unusually convincing case of a free‐living microorganism with a very limited distribution range in the temperate part of eastern North America. The remarkably restricted distribution of N. ansata highlights the extent of our ignorance about the natural history of free‐living microorganisms, and raises questions about the lack of attention to microbial diversity in conservation biology.     

Not all free-living microorganisms have cosmopolitan distributions – the case of Nebela (Apodera) vas Certes (Protozoa: Amoebozoa: Arcellinida)

Aim  To review and critically assess the evidence that the testate amoeba species Nebela vas does not have a cosmopolitan distribution, in contradiction to the paradigm of microbial distribution that 'everything is everywhere'.
Location  Terrestrial and wetland habitats world-wide.
Methods  Relevant data were assembled on the morphology, ecology and global geographical distribution of N. vas from a comprehensive literature review of published original records. The data were collated, analysed and summarized. The roles of long-term and short-term agents of dispersal are discussed.
Results  A clear and repeated pattern has been elucidated of a microbial species, with a distinctive and unmistakeable morphology, that inhabits acid, damp terrestrial and wetland habitats in the southern cool-temperate and sub-Antarctic zones – including similar high-altitude habitats in the Tropics. It is almost entirely confined to the Gondwanaland continents and Southern Hemisphere islands. It is definitively absent from Holarctic regions. It is proposed that the continental distribution of N. vas is a consequence of continental drift following its original speciation in the Mesozoic or earlier, whereas its distribution on sub-Antarctic islands (glaciated in the Pleistocene) has been effected by dispersal from South America by wind around the Southern Ocean.
Main conclusion  Nebela vas is a proven instance of a microbial species that does not have a cosmopolitan distribution.     

The structuring role of microhabitat type in coral degradation zones: a case study with marine nematodes from Kenya and Zanzibar

Nematode genus assemblages were identified from four locations in coral degradation zones (CDZs) along the African east coast: Watamu and Tiwi Beach (Kenya) and Matemwe and Makunduchi (Zanzibar). Three microhabitat types were distinguished: coralline sediment, coral gravel and coral fragments. Nematode community composition was comparable to that of other studies dealing with the same habitat. The presence of a common genus pool in CDZs was reflected in the considerable similarities between samples. The addition of coral fragments as a habitat for nematodes resulted in an increased importance of taxa typical for coarse sediments and large substrata. Local and regional turnover were of the same order of magnitude. The structuring effect of microhabitat type clearly overrode the effect on a local and regional scale. Differences in sediment characteristics were more important in structuring the nematode assemblages than differences between the coralline sediment and coral fragments. No effect related to the three-dimensional structure of coral fragments was found. Differences between nematode assemblages in the coralline sediment and on coral fragments were attributed to the exposed nature of the latter habitat, its large surface area and its microbial or algal cover. Differences in available food sources were reflected in nematode trophic composition.     

基于SD的生态安全指标阈值的确定及应用——以上海崇明岛为例

结合区域复合生态系统的特点,建立由经济、人口、资源、环境和生态5个子系统71个参数构成的上海崇明岛区域生态安全的系统动力学模型,并以变量"净GDP"为参考依据,通过情景仿真进行生态安全趋势分析和方案比较,确定生态安全的指标阈值;通过系统模拟对阈值进行验证,认为阈值在反映系统动态发展趋势上,是一定发展模式下的生态安全的特征参照系。这一尝试克服了目前生态安全指标阈值的研究中以参照法为主的静态性缺憾。将确定的阈值应用于崇明岛生态安全的评价和因子分析中,发现由于崇明岛生态岛的定位和生态保障措施的实施,近几年生态安全综合得分呈现逐步提高的特点,但目前(2007年)得分为0.523,仍处于中等水平;并以阈值为标准的因子检验发现各主要安全因子差异较大,主要的制约因子主要体现为环境治污水平和能源利用等方面。     

Dealing with allometry in linear and geometric morphometrics: a taxonomic case study in the Leporinus cylindriformis group (Characiformes: Anostomidae) with description of a new species from Suriname

To achieve maximum efficacy, taxonomic studies that seek to distinguish amongst species must first account for allometric shape variation within species. Two recently developed software packages (SMATR and MorphoJ) offer regression‐based allometric approaches that are notable for their statistical power and ease of use and that may prove highly useful to taxonomists working with linear or geometric morphometric data. We investigate species delimitation of the slender‐bodied fishes in the Leporinus cylindriformis group using these programs and demonstrate the utility of the allometric corrections that they provide. Without allometric correction, many pairs of species are difficult to distinguish on the basis of morphometrics, but once regressions are used to account for marked allometric variation within species, most of the recognized species in this group can be readily distinguished with linear or geometric morphometrics, particularly using variation in the depth of the body. Both approaches returned congruent patterns of separation amongst putative species, but the geometric approach in MorphoJ distinguished amongst four more pairs of species than did the linear approach in SMATR and appears to provide slightly more statistical power. Based on distinctive morphometrics, meristics, and coloration, a highly elongate species of Leporinus from the Suriname, Corantijn, and Coppename rivers of Suriname is described herein as a new species, Leporinus apollo sp. nov. The unique L. cylindriformis holotype from Porto de Moz, Brazil differs in morphology, meristics, and pigmentation from specimens commonly referred to that species from the main basin of the Amazon; the latter specimens may represent an additional undescribed species. The L. cylindriformis holotype itself may represent a rare species or a specimen collected at the edge of its native range. Measurements of the holotype and paratype of Leporinus niceforoi, which were collected in the Amazonian slope of Colombia, differ substantially from similarly pigmented and putatively conspecific specimens from Amazonian portions of Ecuador and Peru. Recently collected specimens from Colombia are needed to determine whether the observed morphometric variation encompassed by the current concept of L. niceforoi indicates a morphocline within a single species, suggests the presence of multiple cryptic species, or results from shrinkage of the types. In all these cases, linear or geometric morphometric data can reliably differentiate amongst species, but only after one accounts for allometric shape variation. The new SMATR and MorphoJ software packages both offer easy and effective approaches to such allometrically informed taxonomy, and may prove useful to any systematist working on taxa that change shape as they grow. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 103–130.     

The oceanic concordance of phylogeography and biogeography: a case study in Notochthamalus

Dispersal and adaptation are the two primary mechanisms that set the range distributions for a population or species. As such, understanding how these mechanisms interact in marine organisms in particular – with capacity for long‐range dispersal and a poor understanding of what selective environments species are responding to – can provide useful insights for the exploration of biogeographic patterns. Previously, the barnacle Notochthamalus scabrosus has revealed two evolutionarily distinct lineages with a joint distribution that suggests an association with one of the two major biogeographic boundaries (~30°S) along the coast of Chile. However, spatial and genomic sampling of this system has been limited until now. We hypothesized that given the strong oceanographic and environmental shifts associated with the other major biogeographic boundary (~42°S) for Chilean coastal invertebrates, the southern mitochondrial lineage would dominate or go to fixation in locations further to the south. We also evaluated nuclear polymorphism data from 130 single nucleotide polymorphisms to evaluate the concordance of the signal from the nuclear genome with that of the mitochondrial sample. Through the application of standard population genetic approaches along with a Lagrangian ocean connectivity model, we describe the codistribution of these lineages through a simultaneous evaluation of coastal lineage frequencies, an approximation of larval behavior, and current‐driven dispersal. Our results show that this pattern could not persist without the two lineages having distinct environmental optima. We suggest that a more thorough integration of larval dynamics, explicit dispersal models, and near‐shore environmental analysis can explain much of the coastal biogeography of Chile.     

海岛城市化过程中的生态安全动态评价与驱动力分析——以平潭岛为例

随着海岛城市化进程的不断加速,海岛的开发建设与生态安全的矛盾日益突出,客观评价平潭岛开发建设中生态状况的动态变化及驱动力分析,对促进平潭岛社会经济与生态环境的协调发展具有重大意义。选取平潭岛2001年作为生态安全状况评价对比基准年份,另选取2005—2015年的自然与社会经济指标数据构建了平潭岛生态安全评价DPSIR评价指标体系。采用综合指数法发现驱动力因子、影响因子在评价年份中动态变化较为平稳;压力因子、状态因子动态变化趋势较为相似,响应因子在2009年设立综合试验区之前动态变化较为平稳,但是2009—2012年波动最为明显。响应因子、压力因子、状态因子对生态安全指数产生重大影响,其中响应因子是关键因子,对生态安全指数有决定性影响。平潭岛的生态安全状态总体呈上升趋势,2001年、2005—2009年生态安全状况总体上较为平稳,而设立综合实验区以来的2009—2011年期间生态安全指数上升幅度最为明显,尤其是从2011年开始,生态安全指数达到0.7612,生态安全状况由2010年的临界进入了良好,后续2012—2015年呈现略微下降的平稳状态。进行相关因子分析发现状态指数、驱动力指数、响应指数与安全总指数的相关系数较高并且响应指数大于压力指数相关系数;通过主成分分析与通径分析发现2011年与2015年的主成分综合得分最高,分别为1.5277与1.1974,响应因子对平潭岛生态安全状况起到决定作用,其中交通运输投资比率、卫生社会保障投资比率、公共设施投资比率对平潭岛生态安全状况产生直接与间接的影响较大。研究可以丰富海岛环境评估的实证案例与相关理论体系,同时为国内海岛城市化进程的生态安全评估提供借鉴。     

围填海景观格局演变及存量资源分析——以大连长兴岛附近海域为例

以大连市长兴岛附近海域为研究区域,收集1995年、2000年Landsat TM遥感影像及2005年、2010年、2016年高分辨率遥感影像,分析20年来研究区围填海的动态空间分布及景观格局变化特征,建立面向对象的围填海存量资源分类提取方法,并构建围填海存量资源指数,对长兴岛围填海存量资源状况进行分析,得出以下结论:(1)长兴岛附近海域围填海年动态变化在2010—2016年间幅度最大;长兴岛东南部为围填海动态变化的主要区域。(2)整个区域在监测期内表现出多种围填海小型斑块被整合,大型斑块积极向外扩展的发展态势,区域内景观表现出多样性和复杂性增加而优势度减小的趋势。(3)长兴岛附近海域围填海总体利用效率较低,填而未建区域面积最大,其次为围而未填区域及低效工业城镇用海类型,围填海存量资源总面积达到22008.5 hm~2。     

The influence of sampling intensity on the perception of the spatial distribution of tropical diversity and endemism: a case study of ferns from Bolivia

The distribution of tropical plant and animal diversity is still poorly documented, especially at spatial resolutions of practical use for conservation. In the present study, we evaluated the level to which geographical incomplete data availability of species occurrence affects the perception of biodiversity patterns (species richness and endemism) among pteridophytes in Bolivia. We used a data base of Bolivian pteridophytes (27,501 records), divided it into three time periods (1900–70, up to 1990 and up to 2006), and created grid-files at 15'-resolution for species richness and endemism. For each of these biodiversity properties we estimated the species richness (Chao 2) and the index of sampling completeness (C index) per grid, and then all these variables at both species richness and endemism were correlated. Patterns of richness were fairly consistent along all periods; the richest areas were placed along the humid-montane forest, even though they were strongly influenced by collecting intensity. Endemism had a lower degree of correlation with collecting intensity, but varied much more strongly through time than species richness. According to the C index, which gives the ratio between estimated (by Chao 2) and recorded values of species richness and endemism, both biodiversity properties tended to be undersampled in the richest grid cells. Inter-temporal correlations showed sharper differences of correlations for endemism than species richness. Consequently, already in 1970, botanists had a correct idea of the spatial distribution of pteridophyte richness in Bolivia (even though the magnitude was grossly underestimated). In contrast, patterns of endemism, which are of high conservation importance, may not even today be reliably known.     

The role of landscape texture in conservation biogeography: a case study on birds in south-eastern Australia

The binary classification of landscapes into suitable vs. unsuitable areas underlies several prominent theories in conservation biogeography. However, a binary classification is not always appropriate. The textural discontinuity hypothesis provides an alternative theoretical framework to examine the geographical distribution of species, and does not rely on a binary classification scheme. The texture of a given landscape is the combination of its vertical structural complexity and horizontal spatial grain. The textural discontinuity hypothesis states that biophysical features in the environment are scaled in a discontinuous way, and that discontinuities in the body size distribution of animals mirror these biophysical discontinuities. As a result of this relationship, a complex landscape texture should be associated with small‐bodied animals, whereas a simple landscape texture should be associated with larger‐bodied animals. We examined this hypothesis for birds in five landscapes in south‐eastern Australia that represented a gradient from simple to complex landscape texture. In landscapes with a complex texture, the number of detections of small birds was higher than expected, and the number of detections of larger‐bodied birds was lower than expected. The opposite pattern was found in landscapes with a simple texture. The pattern remained significant when only bird species found in each of the five landscapes were considered, which demonstrated that the association of landscape texture with body size was not an artefact of landscapes differing in their species pools. Understanding the effects of landscape texture on species distribution patterns may be a promising research frontier for conservation biogeography. We hypothesize that the active management of landscape texture may be used to attract or deter animals of certain body sizes. Consistent with other theories, the textural discontinuity hypothesis therefore suggests that managing entire landscapes, rather than only predefined patches, is an important conservation strategy.     

Biodiversity assessment: a case study in predicting richness from the potential distributions of plant species in the forests of south-western Australia

Distributions were predicted for 1430 native plant species as part of a biodiversity assessment in the forests of south‐west Western Australia. From these predicted distributions, an index of plant species richness was generated for the forest area. The most common predictors for distribution were found to be climatic surfaces incorporating some aspect of seasonality in temperature and precipitation. Although coarse, the index confirmed existing knowledge of areas of high biodiversity within the study area and introduced a new area, the Blackwood Plateau, for consideration as a conservation reserve with high species richness. An additional survey was conducted to sample actual species richness in 11 test sites. When actual richness was regressed against predicted richness, a significant correlation was obtained if both annuals and geophytes were excluded from the analysis. With refinement of the model and further data collection targeted at areas of low effort, the species richness index is proposed as a useful tool for conservation planning.     

Contribution of external morphology in solving a species complex: The case of Prorocentrum micans, Prorocentrum gracile and Prorocentrum sigmoides (Dinoflagellata) from the Mexican Pacific Coast

Prorocentrum micans Ehrenberg, Prorocentrum gracile Schütt and Prorocentrum sigmoides Böhm are planktonic dinoflagellates present along the Mexican Pacific coast. These three species can be treated as a species complex because of similar shape and size. The taxonomy of the group has been based on cell form and size, the presence or absence of apical spines and the ornamentation of the main valves. A morphometric study of samples from 11 locations from the Mexican Pacific coast and from laboratory cultures is presented. The presence of a mucron (small tooth) in the antapical region of P. gracile and P. sigmoides morphotypes was recorded for the first time. Morphotypes were defined using as the main criteria the size of pores in relation to the size of the depressions on the cell’s surface, the presence of a mucron in the posterior end of the cell and the shape of the valve margins. Results show a clear distinction between the morphotype P. micans and the P. gracile–P. sigmoides. P. sigmoides is suggested to be a junior synonym of P. gracile as no convincing characters could distinguish these two morphotypes.     

Structure and diversity of intertidal benthic diatom assemblages in contrasting shores: a case study from the Tagus estuary1

The structure of intertidal benthic diatoms assemblages in the Tagus estuary was investigated during a 2‐year survey, carried out in six stations with different sediment texture. Nonparametric multivariate analyses were used to characterize spatial and temporal patterns of the assemblages and to link them to the measured environmental variables. In addition, diversity and other features related to community physiognomy, such as size‐class or life‐form distributions, were used to describe the diatom assemblages. A total of 183 diatom taxa were identified during cell counts and their biovolume was determined. Differences between stations (analysis of similarity (ANOSIM), R = 0.932) were more evident than temporal patterns (R = 0.308) and mud content alone was the environmental variable most correlated to the biotic data (BEST, ρ = 0.863). Mudflat stations were typically colonized by low diversity diatom assemblages (H′ ~ 1.9), mainly composed of medium‐sized motile epipelic species (250–1,000 μm³), that showed species‐specific seasonal blooms (e.g., Navicula gregaria Donkin). Sandy stations had more complex and diverse diatom assemblages (H′ ~ 3.2). They were mostly composed by a large set of minute epipsammic species (<250 μm³) that, generally, did not show temporal patterns. The structure of intertidal diatom assemblages was largely defined by the interplay between epipelon and epipsammon, and its diversity was explained within the framework of the Intermediate Disturbance Hypothesis. However, the spatial distribution of epipelic and epipsammic life‐forms showed that the definition of both functional groups should not be over‐simplified.     

The longitudinal distribution and community dynamics of zooplankton in a regulated large river: a case study of the Nakdong River (Korea)

The longitudinal distribution and seasonal dynamics of zooplankton were examined along a 200-km section of the middle to lower Nakdong River, Korea. Zooplankton was sampled twice a month from January 1995 to December 1997 at five sites in the main river channel. There was considerable longitudinal variation in total zooplankton abundance (ANOVA, p < 0.001). All major zooplankton groups (rotifers, cladocerans, copepodids and nauplii) increased significantly with distance downstream along the river. There also were statistically significant seasonal differences in zooplankton abundance at the sampling sites (ANOVA, p < 0.01). Zooplankton abundance was high in spring and fall and low in summer and winter. The seasonal pattern of rotifers was similar to that of total zooplankton. This reflected the fact that rotifers (Brachionus calyciflorus, B. rubens, Keratella cochlearis and Polyarthra spp.) strongly dominated the zooplankton community at all locations. Among the macrozooplankton, small-bodied cladocerans (e.g. Bosmina spp.) dominated; the abundance of large-bodied cladocerans (e.g. Daphnia) was negligible (0–5 ind. l^–1). Among the environmental variables considered, partial residence time seemed to play the most important role in determining characteristics of the river zooplankton community.     

随机森林算法基本思想及其在生态学中的应用——以云南松分布模拟为例

通常来讲,生态学者对于解释生态关系、描述格局和过程、进行空间或时间预测比较感兴趣。这些工作可以通过模拟输出值(响应)与一些特征值(即解释变量)的关系来实现。然而,生态数据模拟遇到了挑战,这是因为响应变量和预测变量可能是连续变量或离散变量。需要解释的生态关系通常是非线性的,并且解释变量之间具有复杂的相互作用关系。响应变量和解释变量存在缺失值并不是不常有的现象,奇异值也经常出现在生态数据中。此外,生态学者通常希望生态模型即要易于建立又易要于解释。通常是利用多种统计方法来分析处理各种各样情景中出现的独特的生态问题,这些模型包括(多元)逻辑回归、线性模型、生存模型、方差分析等等。随机森林是一个可以处理所有这些问题的有效方法。随机森林可以用来做分类、聚类、回归和生存分析、评估变量的重要性、检测数据中的奇异值、对缺失数据进行插补等。鉴于随机森林本身在算法上的优势,将就随机森林在生态学中的应用进行总结,对建模过程进行概述,并以云南松分布模拟研究为例,对其主要功能特点进行案例展示。通过对随机森林的一般术语、概念和建模思想进行介绍,有利于读者掌握本方法的应用本质,可以预见随机森林在生态学研究中将得到更多的应用和发展。